News

2017-07-10. A new publication in Biophysical Journal by Song et al. uses a VCell model to define mechanisms for signal amplification in the PLC/PKC pathway during chemotaxis. Link to the publication and view model details from […]

7-1-2017. CCAM welcomes several undergraduates and a graduate rotation student who are working on projects related to VCell this summer . Undergraduate students include Keeyan Ghoreshi, Anvin Thomas, Natalie de la Garrique and Shahan Kamal […]

VCell was pleased and honored to host its 18th annual VCell Short Course on June 12-14, 2017. Twelve national and international scientists traveled to work with VCell developers and administrators to construct Virtual Cell models based […]

What Is VCell?

VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application. VCell permits construction of models, application of numerical solvers to perform simulations, and analysis of simulation results, offering the choice of multiple physical approximations and simulation technologies to appropriately model a particular system. The BioModel interface provides an intuitive interface to construct models using either pathway diagrams or rules and from a single model of the physiology allows a choice of compartmental (0 dimensions) or spatial (1,2 or3 dimensions) applications of the physiology that can apply stochastic, determistic, or hybrid stochastic/deterministic solvers. Applications are automatically translated into full mathematical descriptions of reaction and diffusion systems and then solved via fully validated numerical methods. A MathModel interface provides a direct interface to develop models using a math description language. VCell supports multiple biophysical mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology.

Who Are We?

The Virtual Cell is currently developed and funded as a National Resource Center, National Resource for Cell Analysis and Modeling (NRCAM), by the National Institute of General Medical Sciences(NIGMS), grant number P41 GM103313. NRCAM continues to develop new technologies for mathematical models of cell and systems biology through development of new physical formulations of biological mechanisms, developing the numerical methods for mathematically simulating these mechanisms, and bulding software infrastructure to deliver these tools for different types of modeling applications including large reaction network applications, spatial applications and detailed molecular interactions. Meet the VCell Team.

Where Are We?

NRCAM, responsible for the development of VCell, resides at The Center for Cell Analysis & Modeling, at UConn Health. CCAM, established in 1994, consists of expertly trained faculty of varying backgrounds. This diverse wealth of knowledge ranges from chemistry, physics, and experimental cell biology to software engineering. Research at CCAM focuses on the development of new approaches for in vivo measurements and manipulation of molecular events within the cell, as well as new computational approaches to organize such data into quantitative models. CCAM is home to the Microscopy Facility, housing numerous extensive fluorescent imaging microscopes, and the High Performance Computing facility.

“A key advantage of Virtual Cell is that the math is performed “behind the scenes”, so the user can focus on the biochemical reactions and biology of interest. Virtual Cell was developed … to be a simple yet powerful tool to allow students and biologists with relatively little math background to perform computational modeling.”
Greenwald EC, Polanowska-Grabowska RK, Saucerman JJ. 2014. Integrating fluorescent biosensor data using computational models. Methods in Molecular Biology:1071:227-48.

“An advantage of the compartmentalized models supported by Virtual Cell is the ease of building complex, but well constrained models that are informed by experimental data.”
Hake, J., P.M. Kekenes-Huskey, and A.D. McCulloch. 2014. Computational modeling of subcellular transport and signaling.
Current Opinion in Structural Biology. 25:92-97.

The Virtual Cell is a software modeling environment for quantitative cell biological research.

Users can create simple or complex multi-layered models with a Java web-based interface. Distinct biological and mathematical frameworks exist within a single graphical interface designed for experimental cell biologists or theoretical biophysicists.